FEB 02, 2021 8:00 AM PST

Keeping an Eye on COVID Clusters With Rapid Sequencing

WRITTEN BY: Tara Fernandez

Contact tracing is a powerful tool used by public health authorities to help slow the spread of infectious diseases such as COVID-19. Those in close contact with infected individuals can swiftly be informed, tested, and advised to self-isolate, thus lowering the risk of the COVID-19 virus spreading further.

Not every case cluster is so easy to track, however. Scientists have found a way of mapping case networks more efficiently, by leveraging one of the virus’s hallmark flaws. 

“Every time the SARS-CoV-2 virus passes from person to person, it may make copying errors that change a couple of its 30,000 genetic letters”, explains Rowena Bull, a researcher from Australia’s University of New South Wales.

“By identifying this genetic variation, we can establish how different cases of coronavirus are linked – to know where a case was potentially picked up from and who they may have given it to.” 

Bull and colleagues have spearheaded the development of a superior method of contact tracing by employing next-generation genome sequencing technologies. This method provides quick answers as to how COVID cases are linked, enabling improved pandemic-control initiatives.

These guidelines, published in Nature Communications, take advantage of nanopore sequencing. Here, subtle changes in an electric current as DNA or RNA traverses a nano-scale hole in a protein called a nanopore are measured. The signals read by this passage of nucleic acids through the nanopore are then decoded and translated into a sequence. 

One of the main benefits of this platform is its speed. Using this technology, developed by Oxford Nanopore Technologies, the entire 30 kilobase-long SARS-CoV-2 genome can be sequenced in just under four hours.

 

 

The new-and-improved form of viral tracking can help trace the origins of variants (such as the highly-contagious UK variant) and bridge the gaps left by traditional epidemiological investigations. It can also be useful in identifying so-called COVID “super-spreaders” in the community. 

Among the concerns around using this relatively new technology for COVID-tracking applications was whether or not it was accurate enough. In their publication, Bull and colleagues demonstrate this not to be the case, detecting variants with >99% sensitivity and >99% precision in a cohort of 157 COVID-positive patient samples.

“Nanopore devices are cheaper, faster, portable and don’t require the lab infrastructure needed by current standard pathogen genomics tools,” said senior author of the study, Ira Deveson, Head of the Genomic Technologies Group. 

“We hope our validation of this protocol will help other public health teams around the world adopt this technology.”

 

Sources: UNSW Sydney, Nature Communications.


 

About the Author
  • Tara Fernandez has a PhD in Cell Biology and has spent over a decade uncovering the molecular basis of diseases ranging from skin cancer to obesity and diabetes. She currently works on developing and marketing disruptive new technologies in the biotechnology industry. Her areas of interest include innovation in molecular diagnostics, cell therapies, and immunology. She actively participates in various science communication and public engagement initiatives to promote STEM in the community.
You May Also Like
MAY 06, 2021
Clinical & Molecular DX
Using Biology as Technology: A Paradigm Shift
MAY 06, 2021
Using Biology as Technology: A Paradigm Shift
Digital networks have changed the world by integrating into almost every aspect of our lives, but they have yet to direc ...
MAY 18, 2021
Genetics & Genomics
Library Prep Methods for SARS-CoV-2 Sequencing: a Summary
MAY 18, 2021
Library Prep Methods for SARS-CoV-2 Sequencing: a Summary
As the SARS-CoV-2 virus continues to mutate, rapid sequencing of COVID-19-positive samples is more critical than ever. N ...
MAY 11, 2021
Clinical & Molecular DX
Every Minute Counts: Opportunities for Faster Blood Culture Results
MAY 11, 2021
Every Minute Counts: Opportunities for Faster Blood Culture Results
Sepsis is one of the most significant challenges in critical care, and early diagnosis is a decisive factor in determini ...
MAY 15, 2021
Neuroscience
Eye Scans May Indicate Early Signs of Alzheimer's
MAY 15, 2021
Eye Scans May Indicate Early Signs of Alzheimer's
Researchers from the University of California San Francisco have found that retinal scans can detect changes in blood ve ...
JUN 04, 2021
Cannabis Sciences
Neurotechnology and Saliva Tests Detect Psychoactive Effects of Cannabis
JUN 04, 2021
Neurotechnology and Saliva Tests Detect Psychoactive Effects of Cannabis
Researchers from contract research organization, KGK Science, working on behalf of neurotechnology firm Zentrela, have f ...
JUL 29, 2021
Genetics & Genomics
Obesity May Not Always Lead to Disease
JUL 29, 2021
Obesity May Not Always Lead to Disease
Some gene variants might be protecting people from the negative health effects of obesity.
Loading Comments...